@include "_cloupe_stages.mro"

call CLOUPE_PREPROCESS(
    pipestance_type = "SC_RNA_COUNTER_CS",
    sample_id = "h2b_run2",
    sample_desc = "",
    analysis = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u85e8949f01/files/analysis",
    filtered_gene_bc_matrices_h5 = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u85e8948a9f/files/filtered_matrices_h5.h5",
    metrics_json = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SUMMARIZE_REPORTS/fork0/chnk0-u85e894a0f3/files/metrics_summary_json.json",
    aggregation_csv = null,
    gem_group_index_json = null,
    no_secondary_analysis = false,
)